A tool that lets you manipulate/convert viral amplicon/primer scheme information.
What is it for?
The layout of (tiled-) amplicon schemes for amplifying and sequencing viral
genomes is typically specified through one of a number of non-standardized
scheme files. These can, generally, not be used interchangeably with downstream
analysis tools.
VirAmp-Hub can convert between commonly used scheme file formats, such as used,
e.g., by the ARTIC network,
the ivar and
cojac suites of tools, and
Galaxy tools and workflows for viral sequencing
data analysis.
Usage
After installation (pip install viramp-hub), use the package via the
scheme-convert command.
For help run:
scheme-convert --help
Prepare an existing primer scheme file for use with ivar:
scheme-convert primer_scheme.bed --to bed --bed-type ivar -o ivar.bed
Generate an amplicon insert scheme file for cojac:
scheme-convert primer_scheme.bed --to bed --bed-type cojac -o cojac_insert.bed
Generate an amplicon info file for use with ivar inside Galaxy:
Amplicon info files are simple tab-separated files listing primers contributing
to the same amplicon on a single line. For nested primer schemes, you can
control, which primers to report in the info file.
VirAmp-Hub tries to autodetect primer to amplicon assignments using the Python
re pattern: r'(?P<prefix>(.*_)*)(?P<num>\d+).*_(?P<name>L(?:EFT)?|R(?:IGHT)?)'.
If this fails for any given primer scheme, it is possible to override
autodetection by providing an amplicon info file directly, e.g.:
scheme-convert primer_scheme.bed -a amplicon_info.tsv --to bed --bed-type cojac -o cojac_insert.bed
or:
scheme-convert primer_scheme.bed -a amplicon_info.tsv --to amplicon-info -r inner -o info.tsv
VirAmp-Hub
A tool that lets you manipulate/convert viral amplicon/primer scheme information.
What is it for?
The layout of (tiled-) amplicon schemes for amplifying and sequencing viral genomes is typically specified through one of a number of non-standardized scheme files. These can, generally, not be used interchangeably with downstream analysis tools.
VirAmp-Hub can convert between commonly used scheme file formats, such as used, e.g., by the ARTIC network, the ivar and cojac suites of tools, and Galaxy tools and workflows for viral sequencing data analysis.
Usage
After installation (
pip install viramp-hub), use the package via thescheme-convertcommand.For help run:
Prepare an existing primer scheme file for use with ivar:
Generate an amplicon insert scheme file for cojac:
Generate an amplicon info file for use with ivar inside Galaxy:
Amplicon info files are simple tab-separated files listing primers contributing to the same amplicon on a single line. For nested primer schemes, you can control, which primers to report in the info file.
List only the inner primers:
List only the outer primers:
VirAmp-Hub tries to autodetect primer to amplicon assignments using the Python re pattern:
r'(?P<prefix>(.*_)*)(?P<num>\d+).*_(?P<name>L(?:EFT)?|R(?:IGHT)?)'. If this fails for any given primer scheme, it is possible to override autodetection by providing an amplicon info file directly, e.g.:or: